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Winston
Hide Associate Professor Harvard School of Public Health Director of the MRC/UWC/SANBI Pathogen Bioinformatics Capacity Development Unit Visiting Extraordinary Professor of Genomics and Bioinformatics, UWC Kerr Fellow, Ludwig Institute for Cancer Research
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| Research Interests |
I am a
computational biologist who seeks to understand
biology using the integration and novel analysis of disparate data
resources. My work focuses upon the discovery of genes and groups
of genes that are involved in disease processes. I apply this approach
to the discovery of genes that contribute to resistance from infection,
and the gene groups that contribute to the process of development and
proliferation of cancers.
Three areas I am working in that are of high impact are (1) The discovery of regulatory networks of transcripts expressed during the proliferation of lineages from cancer stem cells (2) The training and development of people to develop systems for the control of pathogens and vectors such as theTsetse fly, the vector for African sleeping sickness (3) the regulatory events occurring during infection of macrophage All of these are impacted by work in my laboratory on gene expression and its management in the form of ontologies. Together with the researchers I am fortunate to work with at SANBI, and our collaborators in South Africa and my group at Harvard, we are working on defining, characterizing and exploiting high-resolution knowledge of cellular networks involved in cancer and pathogenesis. We achieve this by development and application of systems and tools that allow efficient linkage between interdisciplinary information to result in novel or improved clinical outcomes. SANBI's philosophy embraces development, dissemination, and training in bioinformatics in a community based approach. We develop excellence in people, and have a commitment to professionalism and transparency. |
| Selected Publications from the last 5 years |
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2009
Lal,
A., Navarro, F., Maher, C.A., Maliszewski, L.E., Yan, N., O'Day, E.,
Chowdhury, D., Dykxhoorn, D.M., Tsai, P., Hofmann, O., Becker, K.G.,
Gorospe, M., Hide, W., and Lieberman, J. (2009). miR-24 Inhibits cell
proliferation by targeting E2F2, MYC, and other cell-cycle genes via
binding to "seedless" 3'UTR microRNA recognition elements. Mol Cell 35,
610-625.
2008Howe, D., Costanzo, M., Fey, P., Gojobori, T., Hannick, L., Hide, W., Hill, D.P., Kania, R., Schaeffer, M., St Pierre, S., Twigger, S., White, O., and Rhee, S.Y. (2008). Big data: The future of biocuration. Nature 455, 47-50. Suzuki, H., Forrest, A.R., van Nimwegen, E., Daub, C.O., Balwierz, P.J., Irvine, K.M., Lassmann, T., Ravasi, T., Hasegawa, Y., de Hoon, M.J., Katayama, S., Schroder, K., Carninci, P., Tomaru, Y., Kanamori-Katayama, M., Kubosaki, A., Akalin, A., Ando, Y., Arner, E., Asada, M., Asahara, H., Bailey, T., Bajic, V.B., Bauer, D., Beckhouse, A.G., Bertin, N., Bjorkegren, J., Brombacher, F., Bulger, E., Chalk, A.M., Chiba, J., Cloonan, N., Dawe, A., Dostie, J., Engstrom, P.G., Essack, M., Faulkner, G.J., Fink, J.L., Fredman, D., Fujimori, K., Furuno, M., Gojobori, T., Gough, J., Grimmond, S.M., Gustafsson, M., Hashimoto, M., Hashimoto, T., Hatakeyama, M., Heinzel, S., Hide, W., Hofmann, O., Hornquist, M., Huminiecki, L., Ikeo, K., Imamoto, N., Inoue, S., Inoue, Y., Ishihara, R., Iwayanagi, T., Jacobsen, A., Kaur, M., Kawaji, H., Kerr, M.C., Kimura, R., Kimura, S., Kimura, Y., Kitano, H., Koga, H., Kojima, T., Kondo, S., Konno, T., Krogh, A., Kruger, A., Kumar, A., Lenhard, B., Lennartsson, A., Lindow, M., Lizio, M., Macpherson, C., Maeda, N., Maher, C.A., Maqungo, M., Mar, J., Matigian, N.A., Matsuda, H., Mattick, J.S., Meier, S., Miyamoto, S., Miyamoto-Sato, E., Nakabayashi, K., Nakachi, Y., Nakano, M., Nygaard, S., Okayama, T., Okazaki, Y., Okuda-Yabukami, H., Orlando, V., Otomo, J., Pachkov, M., Petrovsky, N., Plessy, C., Quackenbush, J., Radovanovic, A., Rehli, M., Saito, R., Sandelin, A., Schmeier, S., Schonbach, C., Schwartz, A.S., Semple, C.A., Sera, M., Severin, J., Shirahige, K., Simons, C., St Laurent, G., Suzuki, M., Suzuki, T., Sweet, M.J., Taft, R.J., Takeda, S., Takenaka, Y., Tan, K., Taylor, M.S., Teasdale, R.D., Tegner, J., Teichmann, S., Valen, E., Wahlestedt, C., Waki, K., Waterhouse, A., Wells, C.A., Winther, O., Wu, L., Yamaguchi, K., Yanagawa, H., Yasuda, J., Zavolan, M., Hume, D.A., Arakawa, T., Fukuda, S., Imamura, K., Kai, C., Kaiho, A., Kawashima, T., Kawazu, C., Kitazume, Y., Kojima, M., Miura, H., Murakami, K., Murata, M., Ninomiya, N., Nishiyori, H., Noma, S., Ogawa, C., Sano, T., Simon, C., Tagami, M., Takahashi, Y., Kawai, J., and Hayashizaki, Y. (2009). The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet 41, 553-562. Hofmann,
O., Caballero, O.L., Stevenson, B.J., Chen, Y.T., Cohen, T., Chua, R.,
Maher, C.A., Panji, S., Schaefer, U., Kruger, A., Lehvaslaiho, M.,
Carninci, P., Hayashizaki, Y., Jongeneel, C.V., Simpson, A.J.G., Old,
L.J., and Hide, W. (2008). Genome-wide analysis of cancer/testis gene expression. Proceedings of the National Academy of Sciences of the United States of America 105, 20422-20427.
2007 Computational selection and prioritization of candidate genes for Fetal Alcohol Syndrome.
Zane Lombard, Nicki Tiffin, Oliver Hoffman, Vladimir B Bajic, Winston Hide and Michele Ramsay. BMC Genomics. Adele Kruger, Oliver Hoffman, Winston Hide. Comparison of developmental mammalian gene expression using simplified ontologies. BMC Genomics. 2007 Oct 25;8(1):389 [Epub ahead of print] PMID: 17961254. Simplified ontologies allowing comparison of developmental mammalian gene expression. Kruger A, Hofmann O, Carninci P, Hayashizaki Y, Hide W. Genome Biol. 2007 Oct 25;8(10):R229 [Epub ahead of print] PMID: 17961239 Protein kinase C delta is essential for optimal macrophage mediated phagosomal containment of Listeria monocytogenes Anita Schwegmann, Reto Guler, Antony Cutler, Berenice Arendse, William Horsnell, Andreas Kottmann, Gregory Ryan, Winston Hide, Michael Leitges, Cathal Seoighe and Frank Brombacher Proc Natl Acad Sci U S A. 2007 Oct 9;104(41):16251-6. Epub 2007 Oct 3. PMID: 17913887 Rapid evolution of cancer/testis genes on the X chromosome Stevenson BJ, Iseli C, Panji S, Zahn-Zabal M, Hide W, Old LJ, Simpson AJ, Jongeneel CV. BMC Genomics, 2007. 8: 129. A Model of Directional Selection Applied to the Evolution of Drug Resistance in HIV-1. Cathal Seoighe; Farahnaz Ketwaroo; Visva Pillay; Konrad Scheffler; Natasha Wood; Rodger Duffet; Marketa Zvelebil; Neil Martinson; James McIntyre; Lynn Morris and Winston Hide. Molecular Biology and Evolution 2007; doi: 10.1093/molbev/msm021 2006 Computational disease gene identification: a concert of methods prioritises type 2 diabetes and obesity candidate genes. Nicola Tiffin, Euan Adie, Frances Turner , Han G. Brunner, Marc A. van Driel , Martin Oti , Nuria Lopez-Bigas , Christos Ouzounis , Carolina Perez-Iratxeta , Miguel A. Andrade-Navarro , Adebowale Adeyemo , Mary Elizabeth Patti, Winston Hide. Nucleic Acids Research. Nucleic Acids Res. 2006 Jun 6;34(10):3067-81. Print 2006 Mice and Men: Their Promoter Properties. Vladimir B. Bajic, Sin Lam Tan, Alan Christoffels, Christian Scho¨nbach, Leonard Lipovich, Liang Yang, Oliver Hofmann, Adele Kruger, Winston Hide, Chikatoshi Kai, Jun Kawai, David A. Hume, Piero Carninci, Yoshihide Hayashizaki. PLOS Genetics, April 2006. Volume 2 , Issue 4. The LIFEdb database in 2006 Mehrle A, Rosenfelder H, Schupp I, del Val C, Arlt D, Hahne F, Bechtel S, Simpson J, Hofmann O, Hide W, Glatting KH, Huber W, Pepperkok R, Poustka A, Wiemann S. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D415-8 2005
The Transcriptional Landscape of the Mammalian Genome. The FANTOM Consortium. Science. September 2, 2005 ;309(5740):1559-63. The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms. Tanino M, Debily MA, Tamura T, Hishiki T, Ogasawara O, Murakawa K, Kawamoto S, Itoh K, Watanabe S, de Souza SJ, Imbeaud S, Graudens E, Eveno E, Hilton P, Sudo Y, Kelso J, Ikeo K, Imanishi T, Gojobori T, Auffray C, Hide W, Okubo K. Nucleic Acids Research. 2005 Jan 1;33 Database Issue:D567-72 A case for Glossina genome project. Serap Aksoy, Matt Berriman, Neil Hall, Masahira Hattori, Winston Hide, Michael J. Lehane. Trends in Parasitology, Volume 21, Issue 3 , March 2005, Pages 107-111 2005 Integration of Text- and Data Mining Using Ontologies Successfully Selects Disease Gene Candidates. N. Tiffin, J. Kelso, A. Powell, H. Pan, V. Bajic, W. Hide. Nucleic Acids Research, 2005 33(5): 1544-1552. 2004
Integrative Annotation of 21,037 Human Genes Validated by Full-length cDNA Clones. Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, et al. Public Library of Science Biology 2004 2(6): 1-21 FRAGS: estimation of coding sequence substitution rates from fragmentary data. Estienne C Swart, Winston A Hide and Cathal Seoighe. BMC Bioinformatics 2004 5: 8 2003
Integrative analysis of Intraerythrocytic differentially expressed transcripts yields novel insights into the biology of Plasmodium falciparum. Isokpehi RD and Hide WA. Malaria Journal 2003 2: 38 New Methods for finding disease-susceptibility genes: impact and potential. Mark I McCarthy, Damian Smedley and Winston Hide. Genome Biology 2003 4: 119 Application of eVOC: controlled vocabularies for unifying gene expression data. Winston Hide, Damian Smedley, Mark McCarthy and Janet Kelso. Comptes Rendus Biologies 2003 326(10-11): 1089-1096. Transcriptome Analysis of Mouse Stem Cells and Early Embryos. Alexei A Sharov, Yulan Piao, Ryo Matoba, Dawood B Dudekula, Yong Qian, Vincent VanBuren, Geppino Falco, Patrick R Martin, Carole A Stagg, Uwem C Bassey, Yuxia Wang, Mark G Carter, Toshio Hamatani, Kazuhiro Aiba, Hidenori Akutsu, Lioudmila Sharova, Tetsuya S Tanaka, Wendy L Kimber, Toshiyuki Yoshikawa, Saied A Jaradat, Serafino Pantano, Ramaiah Nagaraja, Kenneth R Boheler, Dennis Taub, Richard J Hodes, Dan L Longo, David Schlessinger, Jonathan Keller, Emily Klotz, Garnett Kelsoe, Akihiro Umezawa, Angelo L Vecovi, Janet Rossant, Tilo Kunath, Brigid LM Hogan, Anna Curci, Michele D Urso, Janet Kelso, Winston Hide and Minoru SH Ko. Public Library of Science Biology 2003 1(3):410-419. eVOC: A Controlled Vocabulary for Unifying Gene Expression Data. Kelso J, Visagie J, Theiler G, Christoffels A, Bardien S, Smedley D, Otgaar D, Greyling G, Jongeneel CV, McCarthy MI, Hide T, Hide W. Genome Research 2003. 13(6): 1220-1230. The S-star Trial Bioinformatics Course. An online Learning Success. Yun Ping Lim, Jan-Olov Hoog, Phyllis Gardner, Shoba Ranganathan, Siv Andersson, Subramanian Subbiah, Tin Wee Tan, Winston Hide and Anthony S. Weiss. Biochemistry and Molecular Biology Education 2003. 31(1): 20-23. The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags. Brentani H, Caballero OL, Camargo AA, da Silva AM, da Silva WA Jr, Dias Neto E, Grivet M, Gruber A, Moreira Guimaraes PE, Hide W, Iseli C, Jongeneel CV, Kelso J, Nagai MA, Ojopi EP, Osorio EC, Reis EM, Riggins GJ, Simpson AJ, de Souza S, Stevenson BJ, Strausberg RL, Tajara EH, Verjovski-Almeida S, Acencio ML, Bengtson MH, Bettoni F, Bodmer WF, Briones MR, Camargo LP, Cavenee W, Cerutti JM, Coelho Andrade LE, Costa dos Santos PC, Ramos Costa MC, da Silva IT, Estecio MR, Sa Ferreira K, Furnari FB, Faria M Jr, Galante PA, Guimaraes GS, Holanda AJ, Kimura ET, Leerkes MR, Lu X, Maciel RM, Martins EA, Massirer KB, Melo AS, Mestriner CA, Miracca EC, Miranda LL, Nobrega FG, Oliveira PS, Paquola AC, Pandolfi JR, Campos Pardini MI, Passetti F, Quackenbush J, Schnabel B, Sogayar MC, Souza JE, Valentini SR, Zaiats AC, Amaral EJ, Arnaldi LA, de Araujo AG, de Bessa SA, Bicknell DC, Ribeiro de Camaro ME, Carraro DM, Carrer H, Carvalho AF, Colin C, Costa F, Curcio C, Guerreiro da Silva ID, Pereira da Silva N, Dellamano M, El-Dorry H, Espreafico EM, Scattone Ferreira AJ, Ayres Ferreira C, Fortes MA, Gama AH, Giannella-Neto D, Giannella ML, Giorgi RR, Goldman GH, Goldman MH, Hackel C, Ho PL, Kimura EM, Kowalski LP, Krieger JE, Leite LC, Lopes A, Luna AM, Mackay A, Mari SK, Marques AA, Martins WK, Montagnini A, Mourao Neto M, Nascimento AL, Neville AM, Nobrega MP, O'Hare MJ, Otsuka AY, Ruas de Melo AI, Paco-Larson ML, Guimaraes Pereira G, Pereira da Silva N, Pesquero JB, Pessoa JG, Rahal P, Rainho CA, Rodrigues V, Rogatto SR, Romano CM, Romeiro JG, Rossi BM, Rusticci M, Guerra de Sa R, Sant' Anna SC, Sarmazo ML, Silva TC, Soares FA, Sonati Mde F, de Freitas Sousa J, Queiroz D, Valente V, Vettore AL, Villanova FE, Zago MA, Zalcberg H; Proceedings of the National Academy of Science. 2003 100(23): 13418-23. 2002
Assembly, verification, and initial annotation of the NIA mouse 7.4K cDNA clone set. Vincent VanBuren, Yulan Piao, Dawood B. Dudekula, Yong Qian, Mark G. Carter, Patrick R. Martin, Carole A. Stagg, Uwem C. Bassey, Kazuhiro Aiba, Toshio Hamatani, George J. Kargul, Amber G. Luo, Janet Kelso, Winston Hide, and Minoru S.H. Ko. Genome Research 2002. 12(12): 1999-2003 Vertical HIV transmission in South Africa: translating research into policy and practice. Salim Abdool Karim, Quarraisha Abdool Karim, Miriam Adhikari, Sharon Cassol, Matthew Chersich, Peter Cooper, Ashraf Coovadia, Hoosen Coovadia, Mark Cotton, Anna Coutsoudis, Win Hide, Greg Hussey, Gary Maartens, Shabir Madhi, Des Martin, John M Pettifor, Nigel Rollins, Gayle Sherman, Stanley Thula, Michael Urban, Sithembiso Velaphi, Carolyn Williamson. The Lancet. March 23, 2002 359: 992-993. Positive Selection Scanning Reveals Decoupling of Ensymatic Activities of Carbamoyl Phosphate Synthetase in H. pylori. Wagied Davids, Junaid Gamieldien, David A Liberles and Winston Hide. Journal of Molecular Evolution. 2002 54: 458-464. Assessment of the Parallelisation approach of d2-cluster for High-Performance Sequence Clustering. John E. Carpenter, Alan Christoffels Yael Weinbach, Winston A. Hide. Journal of Computational Chemistry. 2002 23(7): 755-757. Eukaryotic genes in Mycobacterium tuberculosis could have a role in pathogenesis and immunomodulation. Junaid Gamieldien, Andrey Ptitsyn, Winston Hide. Trends in Genetics 2002 18(1): 5-8. Physical and transcriptional map of the critical region for keratolytic winter erythema (KWE) on chromosome 8p22-p23 between D8S550 and D8S1759. Appel S, Filter M, Reis A, Hennies HC, Bergheim A, Ogilvie E, Arndt S, Simmons A, Lovett M, Hide W, Ramsay M, Reichwald K, Zimmermann W, Rosenthal A. European Journal of Human Genetics. 2002, 10(1): 17-25. Parallelisation of d2-cluster.John Carpenter, Alan Christoffels and Winston Hide. Journal of Computational Chemistry 2002 23(7). 2001
Molecular evolution of Mycobacterium tuberculosis: Phylogenetic reconstruction of clonal expansion. R. M. Warren, M. Richardson, S. L. Sampson, G. D. van der Spuy, W. Bourn, J. H. Hauman, H. Heersma, W. Hide, N. Beyers, P. D. van Helden. Tuberculosis. 2001 81(4): 291-302. Conserved domains of Subtype C Nef from South African HIV type 1-infected Individuals include Cytotoxic T Lymphocyte Epitope-rich regions. Tumelo Mashishi, Shayne Loubser, Winston Hide, Gillian Hunt, Lynn Morris, Gita Ramjee, Salim Abdool-Karim, Carolyn Williamson, Clive M Gray. AIDS Research and Human Retroviruses 2001 17(17): 1681-1687 The contribution of exon-skipping events on Chromosome 22 to Protein Coding Diversity. Winston A. Hide, Vladimir N. Babenko, Peter A. van Heusden, Cathal Seoighe, and Janet F. Kelso. Genome Research. 2001 11: 1848-1853. Profiling the malaria genome: a gene survey of three species of malaria parasite with comparison to other apicomplexan species. Jane M.-R. Carlton, Ralhston Muller, Charles A. Yowell, Michelle R. Fluegge, Kenneth A. Sturrock, Jonathan R. Pritt, Esmeralda Vargas-Serrato, Mary R. Galisnki, John W. Barnwell, Nicola Mulder, Alexander Kanapin, Simon E. Cawley, Winston A. Hide, John B. Dame. Molecular & Biochemical Parasitology 2001 118: 201-210. The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C gram-positive bacteria. Nico C. Gey van Pittius, Junaid Gamieldien, Winston Hide, Gordon D. Brown, Roland J. Siezen, and Albert D. Beyers. Genome Biology 2001 2(10) A platform for genomics in South Africa. Win Hide, Valerie Mizrahi, B Venkatesh, Sydney Brenner, Andrew Simpson, Greg Blatch, Himla Soodyall, Katherine Denby, Mike Wingfield, Brenda Wingfield, Paul van Helden, Raj Ramesar, Rosemary Dorrington, Janet Kelso, Ekow Oppon, Elizabeth Goyvaerts, Michele Ramsay, Etienne de Villiers, Carel van Heerden, Basil Allsopp, Cathal Seoighe. South African Medical Journal. 2001 91(12): 1006-1007. STACKdb: Sequence Tag Alignment and Consensus Knowledgebase. Alan Christoffels, Antoine van Gelder, Gary Greyling, Robert Miller, Tania Hide and Winston Hide. Nucleic Acids Research 2001 29(1): 234-238. |
Rendition of Niviparine mutations induced in HIV Reverse Transcriptase in South African HIV Clade C subjects
